/
parameters.txt
executable file
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/
parameters.txt
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#String that represents the working directory (run_i should be there under ruin folder; the output will be there under "outputs" folder), e.g.:
/Users/Me/MyProject/
#Integer that represents number of runs (the output will be +1 because of the joint)
2
#List of strings that represent the chains
#comma delimited (if more than one) without spaces!
IGH,IGK,IGL
#Integer that represents minimal threshold of reads' length (nucleotides)
300
#Integer that represents minimal threshold of reads' average quality
20
#Integer that represents the k-top clones to be further analyzed
30
#Boolean that indicates whether the samples originated in mice (and not human)
Human
#String that represent the raw data files suffix. txt / xls / etc...
txt
#String that represent the mass_spec_seq to add for the proteomics DB
ASTK
#UMI (IUPAC pattern)
#A single string for forward UMI followed by a comma
#A comma and then a single string for backward UMI (near the constant region)
#Two strings separated by a comma for forward and backward UMIs, e.g.:
HHDACHHDDDDHHNGTCG,AHHDDDHGACAHHDHN